Just installed a BRAND NEW Gates Timing kit to rule out that being the problem and it did not change anything

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Ok so, I just installed a brand new 07 version ej20 longblock with 05 heads, built from the crank out with sti rods by the fourm member riderdude125.

I have 880 Miles on the engine and I noticed the other day when I started it a small knock noise right when the engine fired and then it immediately went away and the car idled normally, I took off and head a knocking type noise sounds like starting at 2500 rpm and can hear it to 3500rpm, then it is either drowned out by the motor and turbo sounds or it goes away. I also noticed that the sound is apparent when holding my foot extremely steady on the gas in one spot at a specific rpm between 2500-3500 and comes and goes as I accelerate and decelerate accordingly. I just replaced this motor and did the oil changes and everything the builder said, im so puzzled and extremely worried being I just spent $3000 on the long block and now im getting another knocking noise . My father owned the car prior to me and just did the timing , which I switched to my new motor maybe 15k to 20k ago .

I also Followed the builder (Casey aka Riderdude125) instructions to a T on break in, and did all the oil changes with Valvoline 5w30 and was planning to switch to t6 rotella after break in. His exact email below

"For start up to prime the oil system you will want to remove the fuel pump relay which is a brown connector on the passenger side right kick panel, it can be kind of tricky to get to. Once the relay is removed you will want to leave the spark plugs and coils off for ease of turning over the motor. Will conventional oil you'll want to crank the motor over for 15 seconds, let it cool, and repeat a couple more times. Install plugs and coils and start the vehicle normally and check for any leaks, ect. Turn off and check oil level and make sure its full. Start vehicle again and let it idle 15-20 to come up to operating temps and make sure your rad fans turn on and off as they should. If all is good you can go for a spin for like 15-25 miles. Change engine oil and filter. Change again at 100 miles, 500 miles and 1000 miles. After that you can do regular intervals with synthetic or whatever oil you prefer. To seat the piston rings you'll want an equal amount of boost and engine breaking, and if possible keep the boost level low. Always vary engine rpms, don't just hop on a highway and cruise at 3500 rpms for a long period of time. Thats really about it, I always say break in a motor like you plan to drive it."

Wow man! After reading/listening I truly feel for you! That's a lot of money and time invested for things to go south. I can't verify if what your builder stated is best for an engine break in as I'm not "internal" knowledgable, but I wanted to at least chime and and wish you the best man!! Hope things work out for you...

No the STi rods and WRX rods have the same big and large ends and are interchangeable(sans the STi rod being beffier), BUT when you start putting things together it's best to have them balanced because even slight factory imbalances are common...
WRX on left STi on right

I'm almost in the same boat. I have a swapped GC with an 03 WRX engine. I had it rebuilt with stock parts. Rebuild was done less then 10k miles ago. I just recently had it e-tuned and about a week ago I started hearing the same type of sound. Sounds almost like a grinding type of noise, sort of noise that you would hear when you have a bad bearing in the transmission, but a much lower sound. I also compare the noise to a fluttering type of noise.